Its likely a view or filter hiding the mail items
If the method above does not work, or if the views are broken or corrupt you can use a command line switch to reset them all back to outlook default settings on install

This is done by opening outlook using
Start>RUn>Outlook.exe /cleanviews

Now note that all views, custom or not, will be reset
If you have any custom views you will need to recreate them

Another thing it could be is a rule
have a look at your rules
note them down (in Detail)

Then open outlook using
Start>RUn>Outlook.exe /cleanrules

this resets all client and server side rules that could move your mailitems out of view

Now go back and re-add your rules
test outlook between each one

if you add one, and the behavior returns
You know its related to that rule and will likely need to modify it